2024_Mentorlist_SimonsSRP


1	2024 SIMONS Summer Research Program at STONY BROOK UNIVERSITY - FACULTY MENTOR LISTING
2	Mentor - Department - Project - Preferred Skills - Link to laboratory/department research page
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4	Dr. Yuefan Deng	Applied Mathematics & Statistics	Developing algorithms in high-performance computing, machine learning, and multiscale modeling for simulations of biological and medical processes.	Physics AP, Math AP, knowledge of basic calculus, programming experience with C, C++ or Python preferred.	https://you.stonybrook.edu/yuefandeng/
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6	Dr. Brian Colle	Atmospheric Sciences	Topics: Future tropical cyclone trends; winter storm research; machine learning applications to weather forecasting	Interested in Earth Sciences; Some programming experience (e.g., Python)	https://you.stonybrook.edu/comap/
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8	Dr. Michael Airola	Biochemistry	Projects in lipid biochemistry include determining the role of membrane environment on the enzymatic activity of lipin phosphatidic acid phosphatases, which are important enzymes in the biosynthesis of phospholipids and triglycerides; protein crystallization and X-ray crystallography		https://cancer.stonybrookmedicine.edu/CancerResearch/Programs/LipidSignaling/Airola
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10	Dr. Benjamin Martin	Biochemistry	The research project will involve studying the maintenance and cell fate determination of stem cells during zebrafish embryonic development. The student will engage in a combination of experimental manipulations and bioinformatic analyses.		https://you.stonybrook.edu/martinlab/
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12	Dr. Aaron Neiman	Biochemistry	Using cell biological and genetic approaches to study the process of sporulation in yeast.		https://www.stonybrook.edu/commcms/biochem/research/_faculty/neiman/#ResearchDescription
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14	Dr. Prateek Prasanna	Biomedical Informatics	Develop machine learning and computer vision tools for characterizing medical images. Potential applications: Tumor segmentation, disease diagnosis, survival prediction, etc.	Strong background in programming, experience in developing machine learning/deep learning models	https://you.stonybrook.edu/imaginelab/
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16	Dr. Alisa Yurovsky	Biomedical Informatics	The students would be involved in exploratory analysis in machine learning with application to precision medicine. This will involve learning to read and present scientific papers and programming.	Background in programming, experience with machine learning/deep learning	https://ayurovsky.github.io/
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18	Dr. Elizabeth Boon	Chemistry	Simons students will work towards understanding the molecular mechanisms by which bacteria regulate biofilm formation. Bacteria have a strong predisposition for growth in a surface-bound, multicellular community called a biofilm, which are implicated in chronic infections of open wounds.		https://www.stonybrook.edu/commcms/chemistry/faculty/_faculty-profiles/boon-elizabeth
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20	Dr. Benjamin Hsiao	Chemistry	Varying projects related to create circular solutions to enhance the nexus of food, water and environment.		www.hsiaoglobal.org
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22	Dr. Iwao Ojima	Chemistry	Research areas include: Medicinal Chemistry, Computer-Aided Drug Design, Drug Disovery, Cancer, Infectious Diseases, Chronic Pain	AP-Chemistry, AP-Biology preferred	https://www.stonybrook.edu/commcms/ojima_group/
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24	Dr. Mohammad Javad Amiri	Computer Science	The student will be engaged in implementing and testing a system that will be used in distributed applications such as blockchains and supply chain management.		https://www3.cs.stonybrook.edu/~amiri/
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26	Dr. Stanley Bak	Computer Science	Formal verification for autonomous (AI) systems, such as small autonomous race cars.		stanleybak.com
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28	Dr. Omar Chowdhury	Computer Science	Projects investigate the security and privacy concerns in 5G core network in a systematic way	Familiarity with a computer programming language like C, C++, Java, or Python; Comfortable working with large code-bases Comfortable with Linux; Familiarity with mathematical logic, although preferred but not necessary; Familiarity with computer security concepts, although preferred but not necessary	https://www.cs.stonybrook.edu/people/faculty/OmarChowdhury
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30	Dr. Michael Ferdman	Computer Science	The COMPAS lab conducts research on computer systems. Our projects develop system-level software and hardware (e.g., Linux kernel extensions, novel CPU hardware organizations, embedded system runtimes, machine learning hardware accelerators, large-scale search engines and file systems).	Programming experience, knowledge of Computer Architecture (CPUs) and Computer Systems (OS).	https://compas.cs.stonybrook.edu/~mferdman/
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32	Dr. Dongyoon Lee	Computer Science	Research projects are offered in the areas of computer systems, security, and software engineering. Possible topics include: C/C++ memory safety, regular expression denial of service, and software testing.	Familiarity with computer programming languages like C, C++, or Python. Basic exposure to Linux/Unix commands.	https://www3.cs.stonybrook.edu/~dongyoon/
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34	Dr. Klaus Mueller	Computer Science	Research projects are offered in areas including: (1) Making algorithmic decision systems fairer through causal network analysis. (2) Exploring how law and policies can improve public health by analyzing socio-economic risk factors. (3) Synthesizing medical images to train/test AI algorithms for medical image diagnostics.	Knowledge of python and possibly javascript will be a plus	https://www3.cs.stonybrook.edu/~mueller/
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36	Dr. Tara Smiley	Ecology & Evolution	Students will work with microCT scans of fossil mammal skulls to infer species ecology in the past. Students will utilize a suite of software tools to process scans, apply ecometric analysis to characterize dental traits, and assess changes in species composition and functional ecology		https://www.tarasmiley.com/
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38	Dr. Ji Liu	Electrical & Computer Engineering	Projects involve algorithm design, analysis, or simulation for (distributed) control, optimization, or machine learning over large-scale complex networks. Possible topics include: distributed control, distributed optimization, distributed machine learning, distributed quantum computing, epidemic networks, social networks.	Requires some mathematical fluency (e.g., Probability, Linear Algebra, Differential Equations) and programming experience (fluent in at least one programming language, e.g., Python and MATLAB).	https://sites.google.com/site/jiliucontrol
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40	Dr. William Holt	Geosciences	The student will perform thermomechanical models of continental deformation using python-based software that is fully developed. The codes can be run in a Jupyter notebook environment. The research will likely target the evolution of the Western United States region over the past 36 million years, including the simulations on the influence of climate, erosion, and sedimentation.	Some desire to conduct numerical modeling in a terminal and Jupyter notebook environtment. The coding language can be learned, but some experience with unix and python may help. The student should be interested in the Earth Sciences.	https://www.stonybrook.edu/commcms/geosciences/people/_faculty/holt.php
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42	Dr. Troy Rasbury	Geosciences	The project will involve characterization of ore deposits associated with fluorite from the southwest United States. This is part of a major on-going NSF funded project to test a hypothesis that geothermal fluids with elevated fluorine concentrations are related to phases of transtension (extension along with strike slip faulting) and produce fluorite and other important critical mineral deposits that can be dated, thus testing the hypothsis which is built on geodynamic modeling. The student would work to characterize these deposits with the Scanning Electron Microscope, with X-Ray Fluorescence element mapping, and with laser ablation inductively coupled plasma mass spectrometry. Together, these willl allow us to learn about mineral associations, element distributions and obtain U-Pb ages for samples with favorable U/Pb ratios.		https://www.stonybrook.edu/commcms/geosciences/people/_faculty/rasbury.php
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44	Dr. Weisen Shen	Geosciences	Research projects include analyzing seismic data collected in the polar regions to study how it illuminates the thermal properties (temperature) beneath the ice and how it affects the ice-sheet movement; and looking at the seismic signature of crustal chemical composition near the geoneutrino sites.		https://www.stonybrook.edu/commcms/geosciences/people/_faculty/shen.php
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46	Dr. Bassem Allam & Dr. Emmanuelle Pales Espinosa	Marine & Atmospheric Sciences	The MADL is a dynamic lab and research currently underway includes shellfish ecology, ecological physiology, shellfish adaptation to climate change, and pathology and immunology, and employs a wide range of techniques and approaches (field studies, genomics, cell and molecular biology).	We do not expect/seek for specific skills, except high enthusiasm!	https://you.stonybrook.edu/madl/people/faculty/bassem-allam/
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48	Dr. Berhane Ghebrehiwet	Medicine	The role of gC1qR and C1q in infection, cancer and autoimmune diseases including Lupus.	Interest in Immunology and experience in some laboratory procedures	https://renaissance.stonybrookmedicine.edu/medicine/rheumatology/laboratorydu/medicine/rheumatology/laboratory
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50	Dr. Joshua Plotkin	Neurobiology	We use cutting edge physiological and imaging techniques to dissect the microcircuitry of the striatum, ask how specific synaptic connections within this circuit are plastically adjusted to optimize behavior, and determine how this is altered in neurological disorders such as OCD.		https://www.stonybrook.edu/commcms/neurobiology/people/faculty_Joshua_Plotkin.php#SelectedPublications
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52	Dr. Howard Sirotkin	Neurobiology	We study proliferation and differentiation of neural stem cells and progenitors, develop animal models for human neurological disorders including Autism, and investigate the neurodevelopmental consequences of environmental pollutants including PFAS "forever chemicals".	AP Biology, Chemistry.	https://www.stonybrook.edu/commcms/neurobiology/people/faculty_Howard_Sirotkin.php#Publications
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54	Dr. David Komatsu	Orthopaedics	Image analysis of bone samples in support of animal studies on skeletal adaption to microgravity.	Familiarity with ImageJ and Excel.	https://renaissance.stonybrookmedicine.edu/orthopaedics/research
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56	Dr. Jessica Seeliger	Pharmacological Sciences	We study diverse aspects of mycobacterial physiology with a focus on processes that contribute to the survival and virulence of the human pathogen Mycobacterium tuberculosis. Much of our work focuses on the mycobacterial cell envelope: how it is made and how it is regulated. A project would be customized as far as possible to the student's interest, experience, and goals.	Previous experience with protein biochemistry (e.g, SDS-PAGE, Western blots), protein expression/purification, or culturing bacteria a plus, but definitely not necessary.	https://renaissance.stonybrookmedicine.edu/pharmacological_sciences/jseeliger_lab
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58	Dr. Dongyan Tan	Pharmacological Sciences	Projects are in the area of chromatin biology and epigenetics, with a focus on using in-vitro assays to investigate the function of various chromatin-associated proteins. Interested students will also have the opportunity to participate in data processing and model building related to structural studies of these proteins using cryo-electron microscopy.		https://www.pharm.stonybrook.edu/faculty_research/directory/t/tan-dongyan
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60	Dr. Eric Jones	Physics & Astronomy	Possible projects in the Laser Teaching Center include trapping and manipulating microscopic objects with optical tweezers, studying systems with geometric optics, and using optical interference in holography.	Calculus, programming in Python (useful but can be learned on the way)	https://laser.physics.sunysb.edu/projects/index.html
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62	Dr. Mengkun Liu	Physics & Astronomy	Topics include: Simulation and machine learning of near-field optics, quantum material research.		https://mengkunliu.wixsite.com/stonybrook
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